Disclaimer : If I owned Atlantis, the boys would spend a LOT more time shirtless or in nothing but towels, Elizabeth would NOT have been taken out, and neither would Carson. Since none of that/all of that has happened, I quite obviously do not own Atlantis or it's characters.

Note : This was inspired by Debbie418uk2's 'Rodney's Really Bad Days'. I loved the imaginative plots of each chapter and how he not only got into the messes, but his friends always managed to get him out of them. Wonderful work, really!

Also, I can't do scottish accents to save my life, so I'm not really going to try. I don't know what ones will have Carson and what chapters will have Keller. I'm also not usually well known for one-shots, so the chapters might vary in length. Oh and I don't have many done. I don't know if these are coming out alright, so I'm just going to post the few I have, one at a time, and see if readers think I should continue or what.

Summary : This fic was inspired by Debbie418uk2's 'Rodney's Really Bad Days'. It's basically a series of one-shots of, well, the title explains it all. John is always getting into trouble, and it's up to his team to save him.

Legend :

"Talking"

Thoughts

(Scene/POV changes)

Pairings : I'm not sure yet, but since each one-shot will likely be more or less unrelated to another, there could be hints of any number of pairings. If any chapter includes a pairing, I will put it at the head of the chapter.

Rating : 'T' for language and situations.

Warnings : Will contain foul language, possibly some adult situations, and graphic scenes (though for the rating, not too graphic).

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(Conversion 2)

"I don't know."

"Oh come on. It's gotta do something."

Leaning against a wall, John sighed as he watched Rodney mess with yet another piece of alien technology. The good part about all this, was that you never knew what these machines could do, and they could seriously benefit Atlantis.

"This could take a while, Colonel." Rodney stated raising an eyebrow at John before returning to his work.

The bad side was that Rodney could take forever in figuring it out.

"I don't get why you're poking at the machine." He pointed out as Rodney held up yet another scanner-type instrument and hovered over the ancient console. "I mean, wouldn't it work better to actually, oh, I dunno..." Walking over, he gestured to the screen and buttons. "Try pressing something?"

"I would expect you to say something like that." He answered dryly, almost glaring at John. "And no, I could end up switching on some sort of self-destruct, or big Wraith 'here I am, come get me' signal, or something."

John couldn't help the small smirk at Rodney's 'Wraith signal' comment before sighing. "Fine, fine. Just hurry up."

As Rodney began scanning all over again, mumbling about this one taking a while, John took a close look at the console. There was a single square screen in the center, surrounded by all kinds of multi-colored buttons. With all the movies he'd seen, touching the big, prominent, red one seemed like a bad idea, but then again, pressing the big green one didn't seem any better.

Still, he felt like he was going to go insane if he didn't do something, so when Rodney had his back turned, John took a close look at the panel and began pressing a few buttons. He was certain it couldn't be as bad as Rodney was making it out to be.

Ok, so this is disappointing. He thought with a raised eyebrow when not even a 'beep' issued forth. "I think this machine's dead."

"No, no, no. It's far from dead. One of my scans showed it's still active." Rodney slowly turned around, his eyes glued to the screen of the scanner he held. "It's like it's-it's in a standby mode or something."

"Well it's not doing anything." John prompted, gesturing to the machine while eyeing the two buttons he didn't press. The red one and the green one. On earth, red means stop or bad. So green would be good, right? Then again, they were on an alien planet, and in an alien city.

"Why would it? We haven't-Sheppard!" Now Rodney looked up. "What the hell are you doing?!"

Removing his hand from the big red button, John carefully looked around, as if expecting everything and nothing at the same time. Again, nothing seemed to happen and he sighed loudly before giving Rodney a pointed look. "See? Dead."

Suddenly, a loud buzz was heard. The machine lit up like a christmas tree and began humming loudly as a series of beeps sounded.

"What did you do?! Damn it John, you just have to touch everything!" Rodney ran over and began rapidly typing stuff on the panel, but nothing seemed to stop the machine.

Then a beam of light erupted from an opening in the wall, and hit John in the chest, knocking him across the room with a pained, startled yelp, and into the wall. Once that had been accomplished, the machine seemed to shut off, leaving John lying unconscious on the ground, and Rodney standing shocked at it all.

It took him a moment, but Rodney finally jumped into action and ran over to the prone colonel. Touching a hand to the side of his neck, the scientist frowned deeply. "Colonel? Sheppard! Damnit!" Finding a faint pulse, he reached up and quickly pressed the button on the comm in his ear. "This is McKay, I need a medical team, stat!"

(Some Time Later, John's POV)

"Ok, that was not fun!" Groaning quietly, I struggled a moment to open my eyes. It took me a few tries, I don't think I've ever been this tired, but I managed to get them open a bit.

Only to slam them shut again.

"Ah, bright!" Another groan, and I slowly lifted my arm to cover my eyes. The feeling of a small pull in the back of my hand, and the sudden knowledge that there was a steady beeping at my right side made me frown deeply. "Where am I?" It smelled kind of...well...sanitary, or of some kind of cleanser, and it hit me.

"Col. Sheppard?"

Opening my eyes again, I struggled to get used to the light as a blurry figure approached the bed I was laying on. Dressed in the standard medical uniform, Carson stood at my bedside.

"How are you feeling?"

"Like I got hit by a hive ship." I muttered as I scrubbed my eyes and tried again. There, that was better. Things were still a little blurry, but at least I could take the light, even if it was giving me a headache. "What happened? I remember..." Squinting, I tried to think. "I was pressing some buttons on one of the machines we found in the new lab."

Carson's face morphed into one that stated 'I should have known'. "Really, Colonel. You know better."

"Yeah, yeah." It felt a little weird, how he was scolding me like a child. "So how am I doing, doc?"

Now he shrugged with a small smile and patted my shoulder. "You'll be fine. I'm running the blood work now, but I think you're alright to go back to your room." His look turned stern. "And that's what I want you to do, John. You need rest, and I don't want you wandering around until I know more about what happened."

So much for feeling reassured. "Got it, doc." I mumbled, already feeling like I was going to pass out again. Damn it, I shouldn't be this tired, should I? Not to mention, as I tried to sit up, my legs felt stiffer, like I hadn't moved them in ages. "How long have I been out?" I asked, feeling incredibly stiff all over, and frowning as Carson removed the IV.

"Only about four hours." He paused a moment and looked at me closely, frowning. "Colonel, is everything alright?"

Staring down at my arms, I tried to figure out why I felt so weird. Five fingers, I wiggled my feet, even though I couldn't see my toes through my socks. Five toes, I hoped. Two arms, two legs, everything seemed in order.

"John?"

"Huh? Oh, right." Looking to Carson, I nodded. "I'm good, just tired."

He nodded reluctantly, and I realized he was borderline ordering me to stay in the infirmary. Not really wanting to make this my new home, I quickly jumped off the bed as he removed the last of the sensors, and grabbed my clothing. "Where's Rodney? And the others?"

"Rodney went back to the machine, to try and find out if there'd be any side effects from the beam that hit you, Ronon went with him. Teyla is filling Dr. Weir in, at the moment."

"'K." With a final nod, and a promise to stay in my room, I made my way out of the infirmary after changing in one of the bathrooms. Stopping in the hallway, I leaned against the wall a moment when a wave of dizziness hit me, and felt my face screw up as this sudden blast of salt hit my sense of smell. Again I frowned, looking around. It might have been late, I didn't see anyone else in the hall. With a shake of my head, the smell and dizziness faded away, and I blamed it on being tired.

Making my way back to my room, I almost sighed in relief as the door slid open, then shut behind me. Looking around, I decided it was too hot to be bundled in my military uniform, and pulled off my jacket. "Someone turn up the heat?" I swiped my hand over the panel, and again when the lights came on, they were blindingly bright. Crying out, I swiped my hand over it again and waited a moment before opening my eyes carefully. "What the hell?!"

Ok, so lights equals bad, right now. Got it. Luckily, I knew my room well enough not to need the lights as I stripped off the rest of my clothing, leaving it on the floor, which was unusual for me. We never knew if spot security checks would be needed, or for some reason or another, people would end up in our rooms, so I'd taken to keeping my room fairly spotless, just in case. Either way, I found myself not bothering to care as I stripped down to my boxers and flopped into bed.

I didn't know how long I lay there. I was exhausted, but I couldn't fall asleep. It felt like hours before I even tried to move, and I found my body once again feeling stiff, only this time it was worse than before, and seemed concentrated in my legs. Whenever I tried to move one, I felt the other moving, as well, but I was just so tired...

Finally, I managed to get comfortable, despite my now being cold. Pulling a blanket over me, I finally drifted off into sleep.

(With the other's, Normal POV)

Elizabeth stood in the briefing room, pacing uncomfortably as the others all seemed to be trying to pass the time. "So you think the machine is some sort of...matter re-configuration machine?"

Rodney nodded quietly as he typed away on his datapad. "Yes, yes. It took a while, but I found it in the ancient database. It's some sort of experimental machine for, well...re-configuring organic masses. Only they mentioned something about never making it to human trials. The rest is garbled, I can't make much sense of it."

"Re-what?" Ronon was leaning against the wall.

"Re-configuration." Elizabeth stated, turning to him as she halted her pacing. "It's like a fancy term of saying 'changing' one thing into another."

"You think Sheppard's gonna change?" he asked with a frown, his hand sliding across his hip to his blaster. "Change into what?"

"I don't know, I don't know." Rodney looked up, almost exasperated. "And I don't know. Look, he wouldn't be in this mess if he'd left it up to me, but he couldn't wait. I'm still tying to figure out what kind of damage it might have done to him, and if it's reversable."

"Dr. Beckett to Dr. Weir."

Everyone looked up as the message was relayed along a public channel of their comm systems.

Tapping her ear piece, Elizabeth nodded. "This is Dr. Weir. What news do you have?"

"Not good, I'm afraid. I need you in the infirmary, immediately."

Nodding to the others, she turned and swipped a hand over the wall panel, opening up the door. "Got it, we're on our way." Heading through almost at a jog, she could hear the others behind her, and prayed it was nothing too serious.

Luckily, with the use of the transporters, the trip didn't take long to get to the infirmary, where Carson was waiting with a grim expression.

"What is going on?" Teyla asked, speaking up as she looked around. "And where is the Colonel?"

"I've sent him back to his room to rest." With a sigh, Carson scrubbed his face before gesturing to a screen behind him. "Which I now believe may have been a mistake." On the screen showed a male humanoid body, and a strange green substance that had pooled in the chest, where John had been hit with the beam.

"That scan was taken when he first arrived, six hours ago. There was a mix up. I thought I had his scans before, ones that looked normal; they were labeled as his, but one of the nurses just informed me, this is his real scan." Hitting a button, it changed to show the green substance moving along his arms and legs. "This was taken four hours ago, before he even woke up." He hit another button, showing thicker strains of the green substance. "This was taken two hours ago. It seems, whatever this stuff is, it's multiplying in his body, and overriding his DNA cells." Looking to the others, Carson frowned. "Sheppard is changing. I don't know what into, but he hasn't a lot of time left."

"You don't think it's another version of the same enzyme that almost changed him into a human iratus bug...?"

He shook his head. "No, his blood work came in, it shows signs of this same substance, but it's not like the enzyme. There are faint similarities, but I've never seen anything like this."

Turning to Rodney, Elizabeth looked horribly grim. "Alright, I need you to go figure out how to reverse whatever this machine did."

"And fast." Carson looked at Rodney as well. "It's only a rough estimate, but I believe he's got less than 24 hours before his transformation is complete." With a nod, Rodney turned and took off. Ronon was about to take off after him, but Elizabeth's voice made him stop cold.

"Ronon. I need you and Teyla to go check on John. See what condition he's in, and if you can get him back to the infirmary." With a curt nod, the last two members of Sheppard's team took off, this time in the general direction of his quarters.

(With Ronon and Teyla)

When they got to Sheppard's quarters, Ronon wanted to bust the door down, but Teyla, with an eyebrow raised, pressed her hand to the chime, to see if he was awake. When they received no answer, Ronon was about to pull his blaster out, to shoot open the door, when Teyla swipped her hand over the panel and the door slid open.

"That's strange." the Satedan muttered as he held his blaster at the ready.

Teyla silently agreed, and the two of them walked quietly into his room. The first thing they noticed was that his clothes were everywhere, which was unusual. They had both been in his room for movie nights before, and they never noticed one article of clothing out in the open, besides the sweater here and there.

"Sheppard?"

There was no response, and the two of them moved closer to the bed. All at once, Ronon crinkled his nose and took a step back. "Ugh, what's that smell?!" It was like a sickly sweet smell.

Gathering her courage, Teyla swiftly walked up to the bed and pulled back the covers, gasping in horror at the sight that lay there. Tapping her ear quickly, she frowned. "Carson, this is Teyla. Col. Sheppard has begun changing, we will be unable to bring him to the infirmary."

There was silence for a moment. "Aye, can you tell me what he's changing into?"

Looking down at the bed, she took a good look in the darkness of the room. "Hold on, I need to turn the lights on to see better. Ronon, can you-"

He'd already crossed the room and swiped his hand over the panel, turning on the lights.

Immediately, John began screaming in agony, his voice sounding much higher pitched than it should have, and he began to thrash around on the bed. Wincing, Teyla covered her ears as Ronon turned the lights back off with a grimace, watching as John's eyes opened and glared at them with an eery violet glow to them.

"Ronon? Teyla! What happened?!" This time it was Elizabeth's voice.

"The Colonel had a bad reaction to the light." Teyla mused out loud. "Still, I believe I can describe... He is covered with a strange slime, it is a milky white color. His legs seem to have fused together into a..." Pausing a moment, she got a good look at him as the said, former legs slithered across the bed spread. "Tail, I believe. His eyes are glowing purple, and his skin seems to have changed to a green tone of some kind."

"He looks like a big bug." Ronon put in helpfully, giving Teyla an innocent look when she raised an eyebrow at him.

(With Rodney, some time later)

"Alright. I think we've figured it out." Sighing in exhaustion, Rodney looked at Zalenka. "I need you to get working on these calibrations, while I go fill the others in. Think you can do that, Zelema?"

"Zalenka."

"Hm? Oh, right, right." Grabbing his things, Rodney seemed very much distracted and obviously was not paying attention. "Zelama. I shouldn't be gone long."

As Rodney practically raced out of the room, Zalenka began cursing to himself in czech.

As Rodney ran to the infirmary, he prayed he wasn't too late, and running through the opening doors, he almost sighed in relief to see everyone in one place. "Ok, I think we got it! The machine's-ohmygod!"

There, in the center of the dimmed room, lay Sheppard. At least, Rodney thought it was Sheppard. His body had almost completely changed, his legs gone, replaced by a slithering tail, and his arms melded to his body, though the arm shape and fingers were still identifiable. He also had wings. Big, green, webbed wings. His face was fairly intact, but for the eyes that had turned completely violet, and the skin which had turned to an odd, milky light green color. It was also shiny, and as if oily, his hair was gone.

"Rodney." Elizabeth's voice was stern. "What have you got?"

Sheppard's eyes were locked on his, or at least, they seemed to be. It was difficult to tell with how they now looked. Swallowing heavily, Rodney forced his eyes away. "We're ready." He felt a little bad for saying it so surely, but right at this moment, he was positive they didn't need 'maybe's and 'but's.

Besides, he was fairly certain it was ready.

(Later)

Everyone was once again gathered in the infirmary, after John had been taken to the room and hit with another blast. The change was remarkably quick, and as soon as he had his wits, and the ability to speak, John ordered Rodney in no uncertain terms to destroy the machine.

"I don't remember much, but I do remember feeling like I slept a week. My whole body was stiff, and my eyes were really sensitive."

"You were changing." Teyla stated quietly.

Raising an eyebrow, John stared at her a moment. "Do I even wanna ask?"

"You were changing into a bug." This time it was Ronon, who didn't seem to notice the grimace on Teyla's face, or how Rodney silently excused himself from the room. He didn't even seem to notice the horrified look on John's face. "Only this time it was different from before. You had a big slug-like tail, like that movie you showed me, Slither? And big wings, and your skin was-"

"OK!" Holding up his hands with a slightly green tint to his face, though this one was normal, he glared at Ronon. "I really don't need to know any more. Thanks."

"You sure? You had this-"

"RONON!"

Grinning a little, Ronon got off the bed he was sitting on and patted John's shoulder. "Good to have you back, buddy."

As he and Teyla left, John rolled his eyes before taking a good look at his arms and legs. Wincing a little, he vowed to personally see to it that machine was completely destroyed, as soon as Carson let him leave the infirmary.

"I hate bugs!"

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Ok, this one was...incredibly long. Sorry about that. I also switched POV's at one point, to see how it turned out. I'm not used to fics like this, but I hope you liked it.

I'll make a note now, I'm thinking of doing quite a few on John's Kirkiness, and how it always turns out bad (at least in my fictions)... Hopefully, this story will work. :)

I had these chapters done before 'Elizabeth's Thoughts', but changed her name once I was corrected about the proper spelling. Please Read and Review. I love your comments and any ideas you might have, and I used constructive critisism to help improve my writing.

Thank you.

Tenshi